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  • I’m going to talk about the minimal information for mouse phenotyping procedures. Mouse phenotype procedures are normally tests performed to discover a symptom in the mouse that relates to a human disease to enable scientific research into finding cures.
  • The scope of this minimal information covers standardising mouse phenotyping across different centres/institutes and consortiums doing high throughput gene knock out projects in Europe, enu screens in Japan and in-bred mouse strains in America.It addresses step by step phenotype procedure information, such as 1- take blood sample, 2- test blood sugar level as well as specifically defining what parameters you are measuring and expect to be recorded. It also defines derived measurements where the scientist in question finds, say, a particular parameters divided by another or area under the curve of a plot scientifically meaningful. Environmental and other metadata such as what manufacturer of the blood glucose analyser are used to provide quality control and validation. Also included is what is the resultant ontology term associated with a particular outcome of a parameter measuring statistically different such as high blood glucose
  • We have XML schemas for the procedures themselves as well as xml for capturing the data produced from the procedures. The procedures are stored in a mysql database containing 72 procedures and over 1800 parameters. The phenotype data is validated against this as it is exported into the Europhenome database which gives you access to the raw and annotated mouse phenotype data generated from primary phenotyping pipelines in EUMODIC
  • This has been developed by the Interphenome consortium with input from the Jackson Laboratory in America as well as the Riken institute in Japan among many others. EUMODIC is a consortium of five international centres that use this to validate data going into EuroPhenome and this is set to be continued in IMPC ( Explain IMPC ?) some quick screen shots
  • This has been developed by the Interphenome consortium with input from the Jackson Laboratory in America as well as the Riken institute in Japan among many others. EUMODIC is a consortium of five international centres that use this to validate data going into EuroPhenome and this is set to be continued in IMPC ( Explain IMPC) some quick screen shots

Mimpp andy Mimpp andy Presentation Transcript

  • MIMPP (Minimal Information for Mouse Phenotyping Procedures )
    Andrew Blake, MRC Harwell
  • Scope
    Standardised Mouse Phenotyping
    High throughput gene knock out projects (EUMODIC and IMPC)
    ENU Screens (RIKEN)
    In-bred mouse strains (MPD)
    Step by Step Phenotype Procedure Information
    Defined measured parameters with options
    Defined derived parameters
    Environmental and other Metadata recorded
    Quality Control and Validation
    Ontology Annotation (Mammalian Phenotype and Entity Quality PATO approaches)
  • Implementation
    - XML Schemas
    PPML
    PDML
    Experiment
    Animal
    Mysql db– EMPReSS empress.har.mrc.ac.uk
    5 Pipelines, 72 Procedures, 1822 Parameters
    PDF, HTML, XML and Web Service access
    Data Validation and export to EuroPhenome database www.europhenome.org
  • Contributors
    InterPhenome
    JAX,
    Riken BRC, Japan
    EUMODIC –EU funded
    5 International Clinics – Harwell (UK), ICS (France), HMGU (German), Sanger (UK) , CMHD (Canada)
    IMPC
  • Questions ?